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ST_RWR

ST_RWR, or source-target random walk with restarts, is a source and target dependent pathway reconstruction algorithm that performs PathRank on the input interactome, using its edge weights, prizes, sources, and targets.

For a random walk with restarts implementation that does not use sources and targets, see RWR.

  • threshold: The number of nodes to have in the final returned subgraph.
  • alpha: The damping factor of the internal PathRank algorithm. This is the probability that RWR randomly chooses a neighbor instead of restarting.

ST_RWR is implemented at https://github.com/reed-compbio/rwr.

Dataset Usage

ST_RWR considers sources and targets. ST_RWR considers interactome directionality, and the output subnetwork is also directed.

Implementation Details

ST_RWR returns a ranked list of nodes: SPRAS returns the induced subgraph from the number of nodes corresponding to the user-specified threshold.

Internally, ST_RWR only takes in directed graphs. SPRAS will automatically convert edges to directed edges as necessary. For more information, see the section on :ref:`algorithm directionality <directionality>`.